Merge branch 'master' into knepley/feature-snes-patch

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'pr1276/tristankonolie/fix_complex_c_cpp/maint' into maint [PR #1276]

* pr1276/tristankonolie/fix_complex_c_cpp/maint:
Fix error with PetscComplex when PETSc is compiled with C and used

Merge branch 'pr1276/tristankonolie/fix_complex_c_cpp/maint' into maint [PR #1276]

* pr1276/tristankonolie/fix_complex_c_cpp/maint:
Fix error with PetscComplex when PETSc is compiled with C and used in C++.

If PETSc is compiled with a C compiler then PetscComplex is typedefed to a C type.
When petscmath.h is used in a C++ file, PetscComplex is initialized as if it were a std::complex independent of what it actually is.
This is fixed by checking if PETSC_HAVE_CXX_COMPLEX is defined before initializing PetscComplex.

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Merge branch 'pr1276/tristankonolie/fix_complex_c_cpp/maint' [PR #1276]

* pr1276/tristankonolie/fix_complex_c_cpp/maint:
Fix error with PetscComplex when PETSc is compiled with C and used in C++.

I

Merge branch 'pr1276/tristankonolie/fix_complex_c_cpp/maint' [PR #1276]

* pr1276/tristankonolie/fix_complex_c_cpp/maint:
Fix error with PetscComplex when PETSc is compiled with C and used in C++.

If PETSc is compiled with a C compiler then PetscComplex is typedefed to a C type.
When petscmath.h is used in a C++ file, PetscComplex is initialized as if it were a std::complex independent of what it actually is.
This is fixed by checking if PETSC_HAVE_CXX_COMPLEX is defined before initializing PetscComplex.

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Fix error with PetscComplex when PETSc is compiled with C and used in
C++

If PETSc is compiled with a C compiler then PetscComplex is typedefed to
a C type. When petscmath.h is used in a C++ file, P

Fix error with PetscComplex when PETSc is compiled with C and used in
C++

If PETSc is compiled with a C compiler then PetscComplex is typedefed to
a C type. When petscmath.h is used in a C++ file, PetscComplex is
initialized as if it were a std::complex independent of what it actually
is. This is fixed by checking if PETSC_HAVE_CXX_COMPLEX is defined
before initializing PetscComplex.

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Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'dalcinl/math-isclose' [PR #1252]

Math: Add PetscIsCloseAtTol()

Merge branch 'master' into haplav/feature-mataij-load-from-hdf5

because I need the test loop fix

Merge branch 'haplav/fix-plex-interpolate-interface-cones' [PR #1227]

* haplav/fix-plex-interpolate-interface-cones:
DMPlexIntepolate: fix orientation of faces in interface
Fixes orientation of face

Merge branch 'haplav/fix-plex-interpolate-interface-cones' [PR #1227]

* haplav/fix-plex-interpolate-interface-cones:
DMPlexIntepolate: fix orientation of faces in interface
Fixes orientation of faces in interface (i.e. order and orientations of the corresponding cones) so that they conform across ranks.

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Sys: define MPI_2INT (PetscMPIInt[2]) if it's not yet defined

Merge branch 'stefano_zampini/petscsystypes' [PR #1198]

* stefano_zampini/petscsystypes:
Add header for sys types used by PETSc.
Provides basic types (e.g PetscInt, PetscScalar, PetscObject etc) for

Merge branch 'stefano_zampini/petscsystypes' [PR #1198]

* stefano_zampini/petscsystypes:
Add header for sys types used by PETSc.
Provides basic types (e.g PetscInt, PetscScalar, PetscObject etc) for compilation units without the need to include the gigantic petscsys.h

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Sys: added petscsystypes.h

should contain basic datatypes and forward declarations for sys objects

complexlib namespaced with petsc

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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Merged petsc/petsc into master

Merge branch 'barry/have-veccuda-to-have-cuda'

Change outdated HAVE_VECCUDA macro to simply HAVE_CUDA for clarity/ease of maintenance.

Commit-type: style-fix

Merged petsc/petsc into master